CTCF is a highly conserved, multi-functional nuclear factor involved both in global genome architecture and in many aspects of gene regulation, latter ranging from the direct gene repression/activation to enhancer blocking and hormone-facilitated silencing. CTCF is an 11-zinc-finger (ZF) DNA-binding protein that coordinates the spatial organization of chromatin with the regulation of gene expression. As we discovered, this control acts through two major mechanisms: either direct regulation of a gene downstream of CTSes or indirect regulation, via the formation of chromatin loops stabilized by CTCF dimerization that affects relationships between the promoter, enhancer and/or imprinted control region (ICR). Dimerization activity of DNA-bound CTCF may potentially be at the core of its activity as a versatile chromatin-bridging and chromatin-looping agent in most cell types, underlying its core biological functions. Furthermore, the loop-forming activity of CTCF can be naturally extended to formation of localized somatic inter-chromosome pairing sites that therefore acquire potential for epigenetic co-regulation such as transcription factories, DNA replication factories, and DNA repair foci. Many other chromatin-anchored functions, such as the establishment of imprinting marks and their reading, X-chromosome inactivation, and apoptosis, are regulated by CTCF. CTCF has emerged as a key facilitator of 3D organization of interphase chromatin, as well as a major player in cell proliferation control. In some cases, the loop-forming activity of CTCF was found to be accompanied/complemented by the more direct regulation of a particular gene. This mixed mode regulation is likely the most appropriate representation of a native gene regulation framework. We also identified a novel CTCF activity that directly links CTCF to transcriptional machinery binding of CTCF to Pol II. This novel pathway provides a mechanism for opening loop-independent transcription start sites for either coding or non-coding transcripts throughout the genome. Mechanistically, the regulated recruitment and the subsequent release of Pol II from a DNA-bound CTCF complex indicates that the CTCF site itself could act as an attenuator and/or promoter in some locations in the genome. While CTCF is mostly known as a regulator of gene expression, our data on its potential functions in heterochromatin and centrosomes, as well as its roles in mitosis and meiosis, suggested a significant housekeeping role of CTCF in genome organization and chromosome segregation. CTCF was previously shown to undergo a variety of posttranslational modifications, and we expanded these studies to characterize novel modifications. Another pathological aspect of the deregulated CTCF occupancy of promoter targets sites is aberrant DNA methylation in cancers. Both of these novel biological roles of CTCF are subjects of ongoing studies in the MPS. We previously analyzed genome-wide CTCF targets for the first time (Cell 2007, vol. 128, pp1231-1245), and the fundamental roles of CTCF in cellular functions were validated by a strong correlation of CTCF target sites (CTS) with gene positions in human genome. By virtue of having so many vital functions CTCF became an essential gene in vertebrates, as CTCF-knockout mice are non-viable (lethality at the very early embryonic stages). With respect to human disease, CTCF is a candidate tumor suppressor gene (TSG);several functional point mutations in the 11ZF DBD of CTCF have been characterized in primary cancers, in combination with the LOH of the CTCF locus. In the past year, we studied several loci in order to understand contributions of CTCF CTSes to their regulation. They included genes important for immune responses, as well as genes with a potential for the development of approaches for cancer treatment. As a general rule, we have found that if a CTCF binding site is located upstream of the transcriptional start site, it tends to play an activator role, while CTSes located downstream of (+1) usually behave as repressors. The gene for catalytic subunit of human telomerase (hTERT) is one of the most prominent genes in this study. It was also recently revealed that up to 22% of genes in a typical human being are regulated in the allele-specific manner, so that same genes on homologous chromosomes are expressed differentially. SNPs are potentially one of the major factors directly underlying allelic variations in gene expression. Upon completion of mapping for sites that bind CTCF in individuals and families, it was established that CTCF binding to SNPs is the potent facilitator of allele-specific expression. This is a major breakthrough in our understanding of the role played by noncoding polymorphisms in the human genome. Moreover, because SNPs are frequently associated with a variety of human syndromes, including rare and neglected diseases, our long-tem goals include GWAS on CTCF binding with respect to SNPs in those syndromes. Finally, we found the correlation between DNAse I-hypersensitive sites and CTCF binding in the HIV genome. Moreover, CpG methylation regions linked to epigenetic regulation of HIV-1 latency also correlated with CTCF binding sites. Thus, these important findings form a strong foundation for systematic research on the CTCF involvement in regulation of viral infections.